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BASH specifications


Unique identifier OMICS_14400
Alternative name BeadArray Subversion of Harshlight
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.30.0
Stability Stable
AnnotationDbi, limma, methods, IRanges, GenomicRanges, BiocStyle, stats4, ggplot2, affy, knitr, reshape2, illuminaio, vsn, beadarrayExampleData, R(>=2.13.0), TxDb.Hsapiens.UCSC.hg19.knownGene, hwriter, Biobase(>=2.17.8), lumi, BiocGenerics(>=0.3.2), BeadDataPackR, illuminaHumanv3.db, gridExtra, ggbio, Nozzle.R1
Maintained Yes



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  • person_outline Andy Lynch <>

Publication for BeadArray Subversion of Harshlight

BASH in publications

PMCID: 5192218
PMID: 28004812
DOI: 10.1038/ncomms13874

[…] thresholds based on the variability of each sample and their proportion of normal contamination. rna analysis was performed using illumina ht-12 v3 platform and analysed with the beadarray package. bash algorithm was employed to correct for spatial artefacts. bead-level data was summarized and a selection of suitable probes based on their quality was done using the re-annotation of the illumina […]

PMCID: 4992321
PMID: 27542606
DOI: 10.1186/s12920-016-0215-4

[…] microarray experiments were analysed using beadstudio® software (illumina, san diego) and r (version 2.6.0) []., during this analysis, image files were loaded using the beadarray package. the bash algorithm was used to remove spatial artifacts []. the algorithm generates a grid of neighbours for each bead and identifies three types of defects: compact, diffuse (regions that contain […]

PMCID: 4960560
PMID: 27457222
DOI: 10.1038/srep29832

[…] with the illumina human v4 annotation. the bead-level data were assessed for integrity at multiple levels. raw image quality was assessed visually, by viewing image plots, and numerically, using the bash algorithm, and weights assigned to each probe., the data were log-transformed and probes summarized to provide probe-set data for downstream analysis. quantile normalisation was applied in order […]

PMCID: 4740813
PMID: 26832224
DOI: 10.1038/ncomms10406

[…] was carried out on illumina human ht12 version 4 arrays. all data analyses were carried out on r using bioconductor packages. raw intensity data from the array scanner were processed using the bash and hulk algorithms as implemented in the bead array package. log2 transformation and quantile normalization of the data were performed across all sample groups. differential expression analysis […]

PMCID: 4605990
PMID: 26491426
DOI: 10.1007/s11306-015-0838-z

[…] human ht12 version 3 arrays. all data analyses used the software r and packages from the bioconductor project (gentleman et al. ). raw intensity data from the array scanner was processed using the bash (cairns et al. ) and hulk algorithms as implemented in the beadarray package (dunning et al. ). log2 transformation and quantile normalisation of the data were performed across all sample […]

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BASH institution(s)
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
BASH funding source(s)
This work was funded by The University of Cambridge, Cancer Research UK; Hutchison Whampoa Limited.

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